Synthesis and reactivity of alpha-thio-beta-chloroacrylamides and alpha-thio-beta-chloroenones

Development of novel synthetic methodology for selective transformation of organic compounds is a central element underpinning organic synthesis with control of chemo-, regio- and stereoselectivity a very high priority. Reactions which can be conducted under mild reaction conditions and, ideally in an environmentally attractive manner, are particularly advantageous. The principal objective of this thesis was to explore the synthesis, reactivity and synthetic utility of a series of α,β-thio-β-chloroenones. The stereochemical features of these transformations and the potential of this novel series of compounds in the synthesis of bioactive compounds were of particular interest. In exploring the reactivity of these compounds, the key transformations included nucleophilic additions and Stille cross-coupling at the β-carbon. Chapter 1 reviews the literature relevant to the research conducted, and focuses in particular on the synthesis of β-chloroenones and related unsaturated carbonyl compounds. The synthesis of chalcone compounds from various precursors is also discussed, with particular emphasis on the use of palladium cross-coupling reactions in the preparation of these compounds. The biological activity of chalcones is also summarised in this chapter. The second chapter delineates the stereoselective synthesis of the novel α-thio-β-chloroenones from the corresponding α-thioketones in a multistep reaction cascade initiated by a NCS-mediated chlorination. A range of both alkyl and aryl β-chloroenones were prepared in this work and the oxidation of these compounds to the corresponding sulfoxides and sulfones is also outlined. The electrophilicity of the β-carbon of the enones was examined in nucleophilic addition/substitution reactions with successful access to a variety of synthetically useful novel adducts including acetals and enaminoketones. Investigation of the synthetic potential of the Stille cross-coupling reaction with the novel α-thio-β-chloroenones was explored and provided an efficient route for the synthesis of a novel series of chalcones. Most importantly this new methodology provided a new and synthetically powerful approach for carbon-carbon bond formation at the β-carbon under mild neutral conditions. A preliminary investigation into the use of these β-chloroenones as dienophiles in Diels-Alder cycloaddition reactions is also discussed in this chapter. Chapter 2 also reports the nucleophilic addition of N, O, S and C nucleophiles to previously described β-chloroacrylamides and their corresponding sulfoxide derivatives. This work builds on previous research carried out in this programme and the reactivity of these β-chloroacrylamides at the sulfide and sulfoxide level is compared. Comparison of the reactivity of the β-chloroacrylamides, in nucleophilic substitution and Stille-coupling, with that of the novel β-chloroenones is of interest. Finally, the biological activity of both the β-chloroenones and the β-chloroacrylamides in terms of cytotoxicity is summarised in Chapter 2. The final chapter, Chapter 3, details the full experimental procedures, including spectroscopic and analytical data for the compounds prepared during this research.

Chemical vapour deposition of complex ferroic oxide thin films

Herein is presented a novel chemical vapour deposition (CVD) route for the fabrication of oxide ferroelectrics. A versatile layer-by-layer growth mode was developed to prepare naturally super-latticed bismuth based materials belonging to the Aurivillius phase family, with which good control over composition and crystal structure was achieved. In chapter 3, the effect of epitaxial strain on one of the very simple oxide materials TiO2 was studied. It has been found that the ultra-thin TiO2 films demonstrate ferroelectric behaviour when grown on NdGaO3 substrates. TiO2 exists in various crystal phases, but none of them show ferroelectric behaviour. The epitaxial strain due to the substrate, changes the crystal structure from tetragonal to orthorhombic which in turn leads to ferroelectric behaviour. In chapter 4, a unique growth method for multiferroic BiFeO3 (BFO) thin films is shown, where a phase pure BFO thin films can be prepared even in the presence of excess bismuth precursor during the growth process. This type of growth is usually called adsorption controlled growth and can be used for growing various bismuth containing compounds, where the volatility of bismuth can create various types of defects. Chapter 5 describes the growth of Bi4Ti3O12 thin films in a layer-by-layer growth mode. In this section, the effect of Bi and Ti precursor flows on the growth of thin films is discussed and it is shown that how change in precursor flows leads to out-ofphase boundary defects during the layer-by-layer growth mode. In chapter 6, the growth of a compound Bi5Ti3FeO15, which is a 1:1 mixture of BiFeO3 and Bi4Ti3O12, is presented. The growth mechanism of Bi5Ti3FeO15 thin films is presented, where the Fe precursor flow was controlled from zero to the insertion of one full BiFeO3 perovskite unit cell into the Bi4Ti3O12 structure in addition, the effect of iron precursor flow on crystalline properties is demonstrated. The methods presented in this thesis can be adopted to grow ferroelectric and multiferroic films for industrial applications.

Theory of the electronic and optical properties of dilute bismide alloys

Dilute bismide alloys, containing small fractions of bismuth (Bi), have recently attracted interest due to their potential for applications in a range of semiconductor devices. Experiments have revealed that dilute bismide alloys such as GaBixAs1−x, in which a small fraction x of the atoms in the III-V semiconductor GaAs are replaced by Bi, exhibit a number of unusual and unique properties. For example, the band gap energy (E g) decreases rapidly with increasing Bi composition x, by up to 90 meV per % Bi replacing As in the alloy. This band gap reduction is accompanied by a strong increase in the spin-orbit-splitting energy (ΔSO) with increasing x, and both E g and ΔSO are characterised by strong, composition-dependent bowing. The existence of a ΔSO > E g regime in the GaBixAs1−x alloy has been demonstrated for x ≳10%, a band structure condition which is promising for the development of highly efficient, temperature stable semiconductor lasers that could lead to large energy savings in future optical communication networks. In addition to their potential for specific applications, dilute bismide alloys have also attracted interest from a fundamental perspective due to their unique properties. In this thesis we develop the theory of the electronic and optical properties of dilute bismide alloys. By adopting a multi-scale approach encompassing atomistic calculations of the electronic structure using the semi-empirical tight-binding method, as well as continuum calculations based on the k•p method, we develop a fundamental understanding of this unusual class of semiconductor alloys and identify general material properties which are promising for applications in semiconductor optoelectronic and photovoltaic devices. By performing detailed supercell calculations on both ordered and disordered alloys we explicitly demonstrate that Bi atoms act as isovalent impurities when incorporated in dilute quantities in III-V (In)GaAs(P) materials, strongly perturbing the electronic structure of the valence band. We identify and quantify the causes and consequences of the unusual electronic properties of GaBixAs1−x and related alloys, and our analysis is reinforced throughout by a series of detailed comparisons to the results of experimental measurements. Our k•p models of the band structure of GaBixAs1−x and related alloys, which we derive directly from detailed atomistic calculations, are ideally suited to the study of dilute bismide-based devices. We focus in the latter part of the thesis on calculations of the electronic and optical properties of dilute bismide quantum well lasers. In addition to developing an understanding of the effects of Bi incorporation on the operational characteristics of semiconductor lasers, we also present calculations which have been used explicitly in designing and optimising the first generation of GaBixAs1−x-based devices.

Allylation of intraerythrocytic hemoglobin by raw garlic extracts.

Recent studies have shown that deoxygenated human red blood cells (RBCs) converted garlic-derived polysulfides into hydrogen sulfide, which in turn produced vasorelaxation in aortic ring preparations. The vasoactivity was proposed to occur via glucose- and thiol-dependent acellular reactions. In the present study, we investigated the interaction of garlic extracts with human deoxygenated RBCs and its effect on intracellular hemoglobin molecules. The results showed that garlic extract covalently modified intraerythrocytic deoxygenated hemoglobin. The modification identified consisted of an addition of 71 atomic mass units, suggesting allylation of the cysteine residues. Consistently, purified human deoxyhemoglobin reacted with chemically pure diallyl disulfide, showing the same modification as garlic extracts. Tandem mass spectrometry analysis demonstrated that garlic extract and diallyl disulfide modified hemoglobin's beta-chain at cysteine-93 (beta-93C) or cysteine-112 (beta-112C). These results indicate that garlic-derived organic disulfides as well as pure diallyl disulfide must permeate the RBC membrane and modified deoxyhemoglobin at beta-93C or beta-112C. Although the physiological role of the reported garlic extract-induced allyl modification on human hemoglobin warrants further study, the results indicate that constituents of natural products, such as those from garlic extract, modify intracellular proteins.

Sensitive detection of H2S using gold nanoparticle decorated single-walled carbon nanotubes.

Herein, we demonstrate that highly sensitive conductometric gas nanosensors for H(2)S can be synthesized by electrodepositing gold nanoparticles on single-walled carbon nanotube (SWNT) networks. Adjusting the electrodeposition conditions allowed for tuning of the size and number of gold nanoparticles deposited. The best H(2)S sensing performance was obtained with discrete gold nanodeposits rather than continuous nanowires. The gas nanosensors could sense H(2)S in air at room temperature with a 3 ppb limit of detection. The sensors were reversible, and increasing the bias voltage reduced the sensor recovery time, probably by local Joule heating. The sensing mechanism is believed to be based on the modulation of the conduction path across the nanotubes emanating from the modulation of electron exchange between the gold and carbon nanotube defect sites when exposed to H(2)S.

Biodeposition and Biogeochemical Processes in Shallow, Mesohaline Sediments of Chesapeake Bay

Stocks of the eastern oyster, Crassostrea virginica, have been declining in Chesapeake Bay since the late 19th century, and current strategies involve restoring culture of Crassostrea virginica on-bottom and in devices suspended within the water column. Sub-tidal suspension culture of Crassostrea virginica in Chesapeake Bay occurs mostly in sheltered inlets and tidal creeks and, thereby, has the potential to influence shallow water biogeochemical processes. To assess the influence of Crassostrea virginica biodeposits and benthic microalgae on sediment nitrogen and phosphorus exchange, field studies with Crassostrea virginica held in aquaculture floats and laboratory experiments were conducted. Enhanced organic nitrogen deposition from Crassostrea virginica biodeposits led to gradual increases in surface sediment nitrogen and pore water ammonium concentrations; however, modifications to pore water concentrations were not always expressed at the sediment-water interface. Benthic microalgae often modulated the influence of biodeposits on sediment nitrogen exchange but, as observed in laboratory experiments, the supply of nitrogen from Crassostrea virginica biodeposits may exceed their biological demand. Organic carbon from biodeposits had varying influences on aerobic respiration but consistently stimulated anaerobic metabolism. Shifts in net phosphorus exchange were driven by this anaerobic remineralization and concentrations of iron and manganese oxy(hydr)oxides, with transitions in fluxes coinciding with changes in benthic photosynthesis and oxidation of surface sediments. Manganese and iron oxy(hydr)oxides from biodeposits supported incorporation of added phosphorus and prevented exchange at the sediment-water interface in the absence of iron-sulfide mineral formation. Differences in the response of shallow water sediments to Crassostrea virginica biodeposits were due to the quality and quantity of biodeposits supplied, as well as the spatial and temporal variability within these sediments. Initial conditions and corresponding reference sediments illustrated the potential for sediment biogeochemistry and nutrient exchange from tidal creek sediments to vary spatially and temporally on relatively small scales. Factors influencing variability within tidal creek sediments were related to shifts in riverine freshwater inputs, macroalgal blooms, nutrient concentrations in overlying waters, and bioirrigation from the clam, Macoma balthica.

Algae-Based Purification of Landfill Biogas Using a CO2 Removal System and Helical Photobioreactor in Series

Biogas is a mixture of methane and other gases. In its crude state, it contains carbon dioxide (CO2) that reduces its energy efficiency and hydrogen sulfide (H2S) that is toxic and highly corrosive. Because chemical methods of removal are expensive and environmentally hazardous, this project investigated an algal-based system to remove CO2 from biogas. An anaerobic digester was used to mimic landfill biogas. Iron oxide and an alkaline spray were used to remove H2S and CO2 respectively. The CO2-laden alkali solution was added to a helical photobioreactor where the algae metabolized the dissolved CO2 to generate algal biomass. Although technical issues prevented testing of the complete system for functionality, cost analysis was completed and showed that the system, in its current state, is not economically feasible. However, modifications may reduce operation costs.

Application of CFD in vacuum dezincing process

Most lead bullion is refined by pyrometallurgical methods - this involves a serics of processes that remove the antimony (softening) silver (Parkes process), zinc (vacuum dezincing) and if need be, bismuth (Betterton-Kroll process). The first step, softening, removes the antimony, arsenic and tin by air oxidation in a furnace or by the Harris process. Next, in the Parkes process, zinc is added to the melt to remove the silver and gold. Insoluble zinc, silver and gold compounds are skimmed off from the melt surface. Excess zinc added during desilvering is removed from lead bullion using one of ghree methods: * Vacuum dezincing; * Chlorine dezincing; or * Harris dezincing. The present study concentrates on the Vacuum dezincing process for lead refining. The main aims of the research are to develop mathematical model(s), using Computational Fluid Dyanmics (CFD) a Surface Averaged Model (SAM), to predict the process behaviour under various operating conditions, thus providing detailed information of the process - insight into its reaction to changes of key operating parameters. Finally, the model will be used to optimise the process in terms of initial feed concentration, temperature, vacuum height cooling rate, etc.

The use of mineral trioxide aggregate in endodontics - status report

Mineral trioxide aggregate (MTA) is a clinical product comprising a mixture of Portland cement and bismuth oxide which is currently used as a root−filling material in dentistry. It has good biological compatibility, is capable of promoting both osteogenesis and cementogensis, and is finding increasing use in endodontic therapy. It is dimensionally stable, and provides an acceptable and durable seal for endodontically treated teeth. This article reviews the chemistry and applications of MTA, and highlights the fact that very little is currently known about the hydration chemistry, phase evolution and stability of this cement in physiological environments. However, biological effects of MTA have been well documented and are considered in detail. The article concludes that this material is a useful addition to the range of materials available for clinical application in endodontics.

Macroalgal blooms alter community structure and primary productivity in marine ecosystems

Eutrophication, coupled with loss of herbivory due to habitat degradation and overharvesting, has increased the frequency and severity of macroalgal blooms worldwide. Macroalgal blooms interfere with human activities in coastal areas, and sometimes necessitate costly algal removal programs. They also have many detrimental effects on marine and estuarine ecosystems, including induction of hypoxia, release of toxic hydrogen sulfide into the sediments and atmosphere, and the loss of ecologically and economically important species. However, macroalgal blooms can also increase habitat complexity, provide organisms with food and shelter, and reduce other problems associated with eutrophication. These contrasting effects make their overall ecological impacts unclear. We conducted a systematic review and meta-analysis to estimate the overall effects of macroalgal blooms on several key measures of ecosystem structure and functioning in marine ecosystems. We also evaluated some of the ecological and methodological factors that might explain the highly variable effects observed in different studies. Averaged across all studies, macroalgal blooms had negative effects on the abundance and species richness of marine organisms, but blooms by different algal taxa had different consequences, ranging from strong negative to strong positive effects. Blooms' effects on species richness also depended on the habitat where they occurred, with the strongest negative effects seen in sandy or muddy subtidal habitats and in the rocky intertidal. Invertebrate communities also appeared to be particularly sensitive to blooms, suffering reductions in their abundance, species richness, and diversity. The total net primary productivity, gross primary productivity, and respiration of benthic ecosystems were higher during macroalgal blooms, but blooms had negative effects on the productivity and respiration of other organisms. These results suggest that, in addition to their direct social and economic costs, macroalgal blooms have ecological effects that may alter their capacity to deliver important ecosystem services.

Exploiting satellite earth observation to quantify current global oceanic DMS flux and its future climate sensitivity

We used coincident Envisat RA2 and AATSR temperature and wind speed data from 2008/2009 to calculate the global net sea-air flux of dimethyl sulfide (DMS), which we estimate to be 19.6 Tg S a21. Our monthly flux calculations are compared to open ocean eddy correlation measurements of DMS flux from 10 recent cruises, with a root mean square difference of 3.1 lmol m22 day21. In a sensitivity analysis, we varied temperature, salinity, surface wind speed, and aqueous DMS concentration, using fixed global changes as well as CMIP5 model output. The range of DMS flux in future climate scenarios is discussed. The CMIP5 model predicts a reduction in surface wind speed and we estimate that this will decrease the global annual sea-air flux of DMS by 22% over 25 years. Concurrent changes in temperature, salinity, and DMS concentration increase the global flux by much smaller amounts. The net effect of all CMIP5 modelled 25 year predictions was a 19% reduction in global DMS flux. 25 year DMS concentration changes had significant regional effects, some positive (Southern Ocean, North Atlantic, Northwest Pacific) and some negative (isolated regions along the Equator and in the Indian Ocean). Using satellite-detected coverage of coccolithophore blooms, our estimate of their contribution to North Atlantic DMS emissions suggests that the coccolithophores contribute only a small percentage of the North Atlantic annual flux estimate, but may be more important in the summertime and in the northeast Atlantic.

DIESE Final Report

The DIESE program (Determination of relevant Indicators for Environmental monitoring: A Strategy for Europe) brought together seven French and British research teams, a private company and the agencies responsible for the management of water bodies of the two countries (ONEMA and the Environmental Agency) in a joint effort to document the ecotoxicological effects related to the presence of chemicals in the environment. To contribute to a better understanding and management of the environment, the program has expanded its efforts to (1) use existing knowledge, or new information acquired during the research program, to identify important biological problems affecting wildlife, (2) increase our understanding of toxicological mechanisms involved and thus be able to identify the causes of the identified dysfunctions and (3) to hone our expertise and vigilance systems in order to better monitor changes in the environment and make appropriate diagnoses. The first part of the program identified clear biological effects, and using biological tests representative of the mechanisms of action of compounds, identified the responsible compounds present in the environment. In connection with the feminization observed in many fish species in European streams, a search for estrogenic and anti-androgenic compounds was conducted. A new test identifying estrogenic compounds has been developed in roach and the ER-Calux test for anti-androgenic effects has been implemented. The results showed that, in addition to biocides such as triclosan and chlorophène, many aromatic hydrocarbon compounds are likely to disturb the physiology of living organisms by interacting with the androgen receptor. Six of these were identified in sediment extracts: benzanthrone, fluoranthene, 1,2- benzodiphenylene sulfide, benzo[a]pyrene, benz[a] anthracene, and 9-phenylcarbazole. The second part of the program aimed at documenting and understanding the mechanisms of action of chemicals leading to physiological changes. This work represents a particular challenge when dealing with molluscs, as knowledge about their physiology and endocrinology is still fragmentary. Thus, new technologies including metabolomic and transcriptomic analyses have been implemented in order to obtain a comprehensive picture of the effects on molluscs. Metabolomic research demonstrated that estrogenic compounds are able to alter the metabolism of eicosanoids and amines, while transcriptomic strategies identified genes whose expression is altered in intersex clams. Because these genes mainly appear as “male” genes, the results suggest that these profound physiological changes result from demasculinisation of male clams. Proteomic studies have also been carried out to elucidate the mechanisms of action of pollutants on fish physiology. These studies generally included a set of molecular marker measurements in an integrative and ecological perspective. The results showed that not only male fish physiology is altered but also female reproductive status is impaired. Moreover, it appeared that other alterations of the fish endocrine system, such as androgenic effects, are at work and that the immune system is also subject to chemical pressure including effects from environmental estrogens. Notably, the immune system, like the endocrine system, seems to show periods of particular sensitivity during development. Measurements on growth and on the general metabolism emphasize the importance of environmental conditions in the physiology of aquatic organisms and in particular the inter-site variability due to temperature,hypoxic conditions, and fish development strategies. They thus provide a unique perspective that allow us to better understand the context and consequences of natural conditions on the population. In a third part of the program, the research conducted had the objective of developing and testing a biomarker strategy to support the environmental management methodologies. Two lanes of specific studies have been followed. The first was to implement, over all or part of the study area, robust biomarkers to establish maps that highlight the water bodies at risk and provide information on sources of compounds and associated disturbances. The second part of the work aimed at exploring methodologies to take advantage of biomarker measurements and to integrate them in a very simple and clear index. Partial or comprehensive maps of the Channel area were produced to report the presence of mutagenic or anti-androgenic compounds in the sediments, intersex fish and clams, and imposex. These maps may remain to be completed and work will be necessary to confront this information in order to learn relevant lessons for management of the environment, a goal that the DIESE program has contributed to by providing some necessary and original information.

Air-sea exchange of methanol and acetone during HiWinGS: Estimation of air phase, water phase gas transfer velocities

The air-sea fluxes of methanol and acetone were measured concurrently using a proton-transfer-reaction mass spectrometer (PTR-MS) with the eddy covariance (EC) technique during the High Wind Gas Exchange Study (HiWinGS) in 2013. The seawater concentrations of these compounds were also measured twice daily with the same PTR-MS coupled to a membrane inlet. Dissolved concentrations near the surface ranged from 7 to 28 nM for methanol and from 3 to 9 nM for acetone. Both gases were consistently transported from the atmosphere to the ocean as a result of their low sea surface saturations. The largest influxes were observed in regions of high atmospheric concentrations and strong winds (up to 25 m s(-1)). Comparison of the total air-sea transfer velocity of these two gases (K-a), along with the in situ sensible heat transfer rate, allows us to constrain the individual gas transfer velocity in the air phase (k(a)) and water phase (k(w)). Among existing parameterizations, the scaling of k(a) from the COARE model is the most consistent with our observations. The k(w) we estimated is comparable to the tangential (shear driven) transfer velocity previously determined from measurements of dimethyl sulfide. Lastly, we estimate the wet deposition of methanol and acetone in our study region and evaluate the lifetimes of these compounds in the surface ocean and lower atmosphere with respect to total (dry plus wet) atmospheric deposition.

Lamellibrachia anaximandrin. sp., a new vestimentiferan tubeworm (Annelida) from the Mediterranean, with notes on frenulate tubeworms from the same habitat

A new species of lamellibrachiid vestimentiferan, Lamellibrachia anaximandri n. sp., has been found in the Eastern Mediterranean, close to cold seeps of fluid carrying dissolved methane and sources of sulfide in superficial sediments. It occurs at about 1100 to 2100 m depth, on some of the mud volcanoes on the Anaximander Mountains, south of Turkey, on the Mediterranean Ridge, south of Crete, and on the Nile deep-sea fan. In addition, it has been obtained from rotting paper inside a sunken ship, torpedoed in 1915 and lying at 2800 m depth, southeast of Crete. Some frenulate pogonophores also occur on the mud volcanoes (including a species of Siboglinum resembling S. carpinei and tubes of other unidentified genera). The new Lamellibrachia is the first vestimentiferan species to be described from the Mediterranean. It differs from L. luymesi taken from the Gulf of Mexico population in the very weak development of collars on its tube and in having a smaller number of pairs of branchial lamellae in the branchial plume. Sequencing of the COI and the mt16S genes confirms a difference at the species level between the new species and L. luymesi, and a difference between these two species and four described species of Lamellibrachia from the Pacific Ocean. The largest individuals of L. anaximandri n. sp. may be many years old, but there are numerous young individuals at some sites, showing that favourable conditions are available for settlement and early growth. The development of the branchial plume in a series of young stages reveals that the sheath lamellae, which are characteristic of the genus Lamellibrachia, begin to form only after the establishment of several pairs of branchial lamellae. Examination of the adult trophosome by transmission electron microscopy shows Gram-negative bacteria without internal stacked membranes, indicating that the symbionts are most probably sulfide oxidizing.

Polycyclic aromatic hydrocarbons (PAHS) (I): Measures of prevention and control

Measures of prevention and control against polycyclic aromatic hydrocarbons (PAHs) focus on an official food control, a code of best practice to reduce PAHs levels by controlling industry and in the development of a chemopreventive strategy. Regulation (EU) 835/2011 establishes maximum levels of PAHs for each food group. In addition, Regulations (EU) 333/2007 and 836/2011 set up the methods of sampling and analysis for its official control. Scientific studies prove that the chemopreventive strategy is effective against these genotoxic compounds effects. Most chemopreventive compounds studied with proven protective effects against PAHs are found in fruit and vegetables.